Leodegario A. Ebron

Quantitative Trait Loci Mapping for Leaf Length and Leaf Width in Rice cv. IR64 Derived Lines

The present study was conducted to identify quantitative trait loci (QTLs) for leaf size traits in IR64 introgression lines (INLs). For this purpose, selected F(2) populations derived from crosses between recurrent parent IR64 and its derived INLs, unique for leaf length and leaf width, were used to confirm QTLs. A total of eight QTLs, mapped on three chromosomes, were identified for the four leaf size traits in six F(2) populations. A QTL for leaf length, qLLnpt-1, in HKL69 was identified around simple sequence repeat (SSR) marker RM3709 on chromosome 1. Two QTLs for flag leaf length, qFLLnpt-2 and qFLLnpt-4, in HFG39 were indentified on chromosomes 2 and 4, respectively. For flag leaf width, a QTL, qFLWnpt-4, in HFG39 was identified around RM17483 on chromosome 4. While another QTL for flag leaf width, qFLWnpt-1, in HFG27 was identified around RM3252 on chromosome 1. A QTL for leaf width, qLWnpt-2, in HKL75 was identified around RM7451 on chromosome 2. For leaf width, two QTLs, qLWnpt-4a, qLWnpt-4b, in HKL48 and HKL99 were identified around RM7208 and RM6909, respectively on chromosome 4. Results from this study suggest the possibilities to use marker-assisted selection and pyramiding these QTLs to improve rice water productivity.

Characterization of near-isogenic lines carrying QTL for high spikelet number with the genetic background of an indica rice variety IR64 (Oryza sativa L.)

Total spikelet number per panicle (TSN) is one of the most important traits associated with rice yield potential. This trait was assessed in a set of 334 chromosomal segment introgression lines (ILs: BC3-derived lines), developed from new plant type (NPT) varieties as donor parents and having the genetic background of an indica-type rice variety IR64. Among the 334 ILs, five lines which had different donor parents and showed significantly higher TSN than IR64 were used for genetic analysis. Quantitative trait locus (QTL) analysis was conducted using F2 populations derived from crosses between IR64 and these ILs. As a result, a QTL for high TSN (one from each NPT donor variety) was detected on common region of the long arm of chromosome 4. The effect of the QTL was confirmed by an increase in TSN of five near-isogenic lines (NILs) developed in the present study. The variation in TSN was found among these NILs, attributing to the panicle architecture in the numbers of primary, secondary and tertiary branches. The NILs for TSN and the SSR markers linked to the TSN QTLs are expected to be useful materials for research and breeding to enhance the yield potential of rice varieties.

Development of Differential Varieties for Blast Resistance in IRRI-Japan Collaborative Research Project

In the IRRI-Japan Collaborative Research Project, four kinds of differential varieties, monogenic lines and near isogenic lines (NILs) with three kinds of genetic backgrounds have been developed for the following 24 resistance genes Pia, Pib, Pii, Pik, Pik-h, Pik-m, Pik-p, Piks, Pish, Pita, Pita-2, Pit, Piz, Piz-5 (Pi2), Piz-t, Pi1, Pi3, Pi5(t), Pi7, Pi9 (t), Pi11 (t), Pi12 (t), Pi19 (t), and Pi20. Monogenic lines that have only a single resistance gene in each background, were developed from one to three time’s backcrosses between donor varieties and a Japonica-type variety Lijianxintuanheigu (LTH) as a recurrent parent, and were distributed as first universal differential varieties and gene sources from the International Rice Research Institute (IRRI). Two kinds of NILs with Lijianxintuanheigu (LTH) and US2 genetic backgrounds have also only one resistance gene each. The NILs of an Indica-type variety CO39 are including an additional gene Pia in the genetic background. These NILs are confirming fixations of target resistance gene and morphological characters in the advanced generations BC6F7 or more, and will be released in the near future.

A set of near-isogenic lines of Indica-type rice variety CO 39 as differential varieties for blast resistance

Twenty-seven near-isogenic lines (NILs) with the genetic background of a blast-susceptible variety, CO 39, were developed by repeated backcrossing as a first set of a large number of differential varieties (DVs) with Indica-type genetic background. The NILs included 14 resistance genes—Pish, Pib, Piz-5, Piz-t, Pi5(t), Pik-s, Pik, Pik-h, Pik-m, Pik-p, Pi1, Pi7(t), Pita, and Pita-2—derived from 26 donor varieties. The reaction patterns of NILs against 20 standard isolates from the Philippines were similar to those of blast monogenic lines with the same resistance gene, except for those against two isolates that are avirulent to Pia in the genetic background of CO 39. A genome-wide DNA marker survey revealed that chromosome segments were introgressed in the regions where each resistance gene was previously mapped and most of the other chromosome regions in each NIL were CO 39 type. Segregation analysis of resistance and co-segregation analysis between resistance and DNA markers using F3 populations derived from the crosses between each NIL and the recurrent parent, CO 39, revealed a single-gene control of resistance and association between resistance and target introgressed segments. The morphological characters of each NIL were almost the same as those of the recurrent parent except for some lines, suggesting that these NILs can be used even under tropical conditions where Japonica-type DVs are not suitable for cropping. Thus, these NILs are useful not only as genetic tools for blast resistance study but also as sources of genes for breeding of Indica-type rice varieties.

Quantitative Trait Loci (QTL) Reactions to Rice Blast Isolates from Japan and the Philippines

fourteen qtl for philippine isolates and 12 qtl for japanese isolates were detected in the 14 regions on nine chromosomes (1, 2, 3, 6, 7, 8, 9, 11, and 12) using recombinant inbred lines derived from a cross between indica-type rice milyang 23 and a japonica-type rice akihikari. Among them, several qtl were detected to be common to philippine and japanese isolates. The qtl in two regions on the short arm of chromosome 1 and in the middle of chromosome 6 showed the resistance to philippine and japanese blast isolates, respectively. These qtl on chromosomes 1 and 6 were estimated to correspond to pish and piz-t, respectively. Based on the reaction patterns of detected qtl for japanese and philippine blast isolates, we suggested that pish and piz alleles might have the specified reactions, depending on the origin isolates of temperature or tropical area.

Identification of blast resistance genes in elite Indica-type varieties of rice (Oryza sativa L.).

Eight blast resistance genes --Pia, Pib, Pik-s, Pik-h, Pita, Piz-t, Pi20, and one of three (Pii, Pi3, or Pi5(t)) were identified in 42 IRRI-bred varieties following a differential system using Philippine blast isolates. Among these genes, two genes Pib and one of Pik alleles (Pik-s or Pik-h), were found in almost all IRRI varieties. The number of resistance genes in each variety varied from two to five, and the kinds of gene combination were also limited. This limitation might be due to the gene sources such that IR8, IR24, IR36, or their hybrid progenies were often included in the breeding of these varieties. Using the genefor-gene theory, this study was carried out in three steps: 1) estimation of genes following the reaction patterns of monogenic lines to blast isolates, 2) genetic analysis using BC1F2 populations with a susceptible variety as recurrent parent, and 3) allelism test with Japanese differential varieties. Through genetic analysis, each investigation’s ability to identify resistance genes was demonstrated.

DNA Marker Analysis of Blast Resistance Genes Pib and Pita in IRRI-Bred Rice Varieties Comparing with Gene Estimation by a Differential System

Blast resistance genes are important in rice (Oryza sativa L.) improvement programs. The DNA markers linked to resistance genes are a powerful tool to detect the presence of genes and are widely used to select breeding materials through marker-assisted selection. This study was conducted to evaluate the detection ability of DNA markers for rice blast resistance genes Pib and Pita in IRRI-bred rice varieties. Forty-two Indica-type varieties, which have been previously analyzed for the presence of Pib and Pita by conventional genetic analysis using a differential system involving standard blast isolates (Pyricularia grisea Sacc.) from the Philippines, were tested. To estimate the presence of Pib and Pita, previously reported PCR-based dominant markers were used. The target DNA fragments of Pib using Sub3-5 were amplified in 40 varieties but not in two varieties. Also, the target DNA fragments of Pita using three gene-specific markers were amplified in 27 or 28 varieties but not in 14 or 15 varieties. The results of DNA marker analysis of the 42 IRRI-bred rice varieties were almost the same as those of previous gene estimation of Pib and Pita by the differential system. It suggests that the efficiency of detecting blast resistance genes through use of DNA markers depends on the rice variety and the DNA markers. The proper markers for the Pita gene provide a basis for stacking other blast resistance genes into high-yielding and good-quality advanced breeding rice lines.

Studies on Partial Resistance to Rice Blast in the Tropics

Partial resistance to blast has not been clearly distinguished from major gene resistance in the tropics. Several major genes for resistance to blast were identified recently in IR varieties at the International Rice Research Institute (IRRI) and the reactions of these genes to the Philippine blast isolates were studied. Consequently, suitable blast isolates could be selected to eliminate the effect of these major genes for evaluating partial resistance to blast under field conditions. Seventy-two varieties and breeding lines were inoculated with three blast isolates during two seasons. Serious blast infection was induced by partial shading, continuous irrigation and the application of large amount of fertilizer. Disease damage was evaluated using the Standard Evaluation System (SES) for rice blast. Partial resistance was clearly distinguished from major gene resistance and the differences between moderate levels of resistance conferred by major genes and partial resistance were clarified. Among the materials used, IR64 showed high level of partial resistance. Partial resistance was moderate in IR60 and IR36 and low in IR50 and CO39. These results were consistent with the results of sequential planting done at IRRI earlier. Partial resistance levels of several Japanese varieties at IRRI were also consistent with their evaluations in Japan. Significant positive correlations observed among partial resistance to the three isolates indicate that partial resistance is horizontal in the tropics. Distinction between major gene and partial resistance to blast is necessary for identifying donors for developing durably resistant varieties.